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Title: Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

Abstract

A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb{sup +} and Sr{sup 2+}) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data atmore » q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein–Zernike equations, with results from the Kovalenko–Hirata closure being closest to experiment for the cases studied here.« less

Authors:
 [1]; ; ;  [2]
  1. BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854 (United States)
  2. School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 (United States)
Publication Date:
OSTI Identifier:
22314267
Resource Type:
Journal Article
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 141; Journal Issue: 22; Other Information: (c) 2014 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0021-9606
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; ATOMIC MODELS; CALIBRATION; LIQUIDS; LYSOZYME; MOLECULAR DYNAMICS METHOD; MYOGLOBIN; SMALL ANGLE SCATTERING; SOLUTIONS; WATER; X RADIATION; X-RAY DIFFRACTION

Citation Formats

Nguyen, Hung T., Pabit, Suzette A., Meisburger, Steve P., Pollack, Lois, Case, David A., E-mail: case@biomaps.rutgers.edu, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854. Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids. United States: N. p., 2014. Web. doi:10.1063/1.4896220.
Nguyen, Hung T., Pabit, Suzette A., Meisburger, Steve P., Pollack, Lois, Case, David A., E-mail: case@biomaps.rutgers.edu, & Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854. Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids. United States. https://doi.org/10.1063/1.4896220
Nguyen, Hung T., Pabit, Suzette A., Meisburger, Steve P., Pollack, Lois, Case, David A., E-mail: case@biomaps.rutgers.edu, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854. 2014. "Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids". United States. https://doi.org/10.1063/1.4896220.
@article{osti_22314267,
title = {Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids},
author = {Nguyen, Hung T. and Pabit, Suzette A. and Meisburger, Steve P. and Pollack, Lois and Case, David A., E-mail: case@biomaps.rutgers.edu and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854},
abstractNote = {A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb{sup +} and Sr{sup 2+}) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data at q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein–Zernike equations, with results from the Kovalenko–Hirata closure being closest to experiment for the cases studied here.},
doi = {10.1063/1.4896220},
url = {https://www.osti.gov/biblio/22314267}, journal = {Journal of Chemical Physics},
issn = {0021-9606},
number = 22,
volume = 141,
place = {United States},
year = {Sun Dec 14 00:00:00 EST 2014},
month = {Sun Dec 14 00:00:00 EST 2014}
}